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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGAGAGAGAAATCGAAGCCGTCTTCCTCCGCTCCGGCATCTCGCCTCTTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttccttcgtttcgtcgtcatcgcgcggtattgtcctgcgtttgccgattttttgctgacgtgatggtgtggcgtggcgtgggtggggcaag

Basic information

species Oryza sativa
transcript LOC_Os01g43170.2
intron # 1
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88401621|gb|CI588562.1|CI588562
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88392333|gb|CI612807.1|CI612807
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88434195|gb|CI589260.1|CI589260
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|58672532|gb|CK061218.1|CK061218
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCTCAGACTCGCAGCTCTCGCAAAG                         ATTGA----C--GG--GCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88359026|gb|CI619530.1|CI619530
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGAAGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88360620|gb|CI620355.1|CI620355
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88402140|gb|CI614983.1|CI614983
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88372229|gb|CI619559.1|CI619559
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88401991|gb|CI593703.1|CI593703
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTTGACGGGCGAGGAAGCGAGGAGTGCGTATCTTGGGTGGGTGCGGGGAT
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagA-TTGACGGGCGAGGAAGCGAGGAG-GCGTATCTTGGGTGGGTGCGGGGAT
EST: gi|88723827|gb|CI745524.1|CI745524
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88399395|gb|CI606016.1|CI606016
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88417614|gb|CI581637.1|CI581637
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88311840|gb|CI577446.1|CI577446
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88394784|gb|CI622658.1|CI622658
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88371532|gb|CI602710.1|CI602710
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88393225|gb|CI616709.1|CI616709
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88397912|gb|CI583230.1|CI583230
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88694575|gb|CI738613.1|CI738613
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88337084|gb|CI628170.1|CI628170
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88717456|gb|CI740966.1|CI740966
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88350834|gb|CI619092.1|CI619092
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|29681003|gb|CB677278.1|CB677278
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCGGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|88311951|gb|CI577557.1|CI577557
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAG                         ATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
EST: gi|58611208|gb|CK038920.1|CK038920
EST:     TTCCCATCGCCGCCACCGCCGGCGGTCTCAGACTCGCAGCTCTCGCAAAG                         ATTGA----C--GG--GCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG
genomic: TTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttcc ... gtggggcaagATTGACGGGCGAGGAAGCGAGGAGGCGTATCTTGGGTGGGTGCGGGGATGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGAGAGAGAAATCGAAGCCGTCTTCCTCCGCTCCGGCATCTCGCCTCTTCCCATCGCCGCCACCGCCGGCGGTCGCAGACTCGCAGCTCTCGCAAAGgtgaggttccttcgtttcgtcgtcatcgcgcggtattgtcctgcgtttgccgattttttgctgacgtgatggtgtggcgtggcgtgggtggggcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG